Papers, Pre/Post-Prints, and Presentations by Faculty in the Department of Biomedical Engineering

Recent Submissions

  • The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants 

    Wóycicki, Rafał; Witkowicz, Justyna; Gawroński, Piotr; Dąbrowska, Joanna; Lomsadze, Alexandre; Pawełkowicz, Magdalena; Siedlecka, Ewa; Yagi, Kohei; Pląder, Wojciech; Seroczyńska, Anna; Śmiech, Mieczysław; Gutman, Wojciech; Niemirowicz-Szczytt, Katarzyna; Bartoszewski, Grzegorz; Tagashira, Norikazu; Hoshi, Yoshikazu; Borodovsky, Mark; Karpiński, Stanisław; Malepszy, Stefan; Przybecki, Zbigniew (Georgia Institute of TechnologyPublic Library of Science, 2011)
    Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to ...
  • Harnessing systems biology approaches to engineer functional microvascular networks 

    Sefcik, Lauren S.; Wilson, Jennifer L.; Papin, Jason A.; Botchwey, Edward A. (Georgia Institute of TechnologyMary Ann Liebert, Inc., 2010)
    Microvascular remodeling is a complex process that includes many cell types and molecular signals. Despite a continued growth in the understanding of signaling pathways involved in the formation and maturation of new blood ...
  • Tumor vascular permeability to a nanoprobe correlates to tumor-specific expression levels of angiogenic markers 

    Karathanasis, Efstathios; Chan, Leslie; Karumbaiah, Lohitash; McNeeley, Kathleen; D’Orsi, Carl J.; Annapragada, Ananth V.; Sechopoulos, Ioannis S.; Bellamkonda, Ravi Venkat (Georgia Institute of TechnologyPublic Library of Science, 2009)
    Background. Vascular endothelial growth factor (VEGF) receptor-2 is the major mediator of the mitogenic, angiogenic, and vascular hyperpermeability effects of VEGF on breast tumors. Overexpression of VEGF and VEGF receptor-2 ...
  • Self-similarity in NMR Spectra: An Application in Assessing the Level of Cysteine, 

    Jung, Yoon Young; Park, Youngja; Jones, Dean P.; Ziegler, Thomas R.; Vidakovic, Brani (Georgia Institute of TechnologyData Science Trust, 2010-01)
    High resolution of NMR spectroscopic data of biosamples are a rich source of information on the metabolic response to physiological variation or pathological events. There are many advantages of NMR techniques such as the ...
  • caCORRECT2: improving accuracy and reliability of microarray data in the presence of artifacts 

    Moffitt, Richard A.; Yin-Goen, Qiqin; Stokes, Todd H.; Parry, R. M.; Torrance, James H.; Phan, John H.; Young, Andrew N.; Wang, May D. (Georgia Institute of TechnologyBioMed Central, 2011)
    Background. In previous work, we reported the development of caCORRECT, a novel microarray quality control system built to identify and correct spatial artifacts commonly found on Affymetrix arrays. We have made recent ...
  • ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses 

    Stokes, Todd H.; Torrance, J. T.; Li, Henry; Wang, May D. (Georgia Institute of TechnologyBioMed Central, 2008)
    Background. A survey of microarray databases reveals that most of the repository contents and data models are heterogeneous (i.e., data obtained from different chip manufacturers), and that the repositories provide only ...
  • Histological image classification using biologically interpretable shape-based features 

    Kothari, Sonal; Phan, John H.; Young, Andrew N.; Wang, May D. (Georgia Institute of TechnologyBioMed Central, 2013)
    Background: Automatic cancer diagnostic systems based on histological image classification are important for improving therapeutic decisions. Previous studies propose textural and morphological features for such systems. ...
  • Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi 

    Xu, Junhuan; Linning, Rob; Fellers, John; Dickinson, Matthew; Zhu, Wenhan; Antonov, Ivan; Joly, David L.; Donaldson, Michael E.; Eilam, Tamar; Anikster, Yehoshua; Banks, Travis; Munro, Sarah; Michael Mayo,; Brian Wynhoven,; Ali, Johar; Richard Moore,; McCallum, Brent; Borodovsky, Mark; Saville, Barry; Bakkeren, Guus (Georgia Institute of TechnologyBioMed Central, 2011)
    Background.Rust fungi are biotrophic basidiomycete plant pathogens that cause major diseases on plants and trees world-wide, affecting agriculture and forestry. Their biotrophic nature precludes many established molecular ...
  • Bacillus anthracis genome organization in light of whole transcriptome sequencing 

    Martin, Jeffrey; Zhu, Wenhan; Passalacqua, Karla D.; Bergman, Nicholas; Borodovsky, Mark (Georgia Institute of TechnologyBioMed Central, 2010)
    Emerging knowledge of whole prokaryotic transcriptomes could validate a number of theoretical concepts introduced in the early days of genomics. What are the rules connecting gene expression levels with sequence determinants ...
  • Mechanistic Interrogation of Phthalimide Neovascular Factor 1 using Network Analysis Tools 

    Wieghaus, Kristen A.; Gianchandani, Erwin P.; Brown, Milton L.; Papin, Jason A.; Botchwey, Edward A. (Georgia Institute of TechnologyMary Ann Liebert, Inc., 2007-10)
    Neovascularization is essential for the survival and successful integration of most engineering tissues after implantation in vivo. The objective of this study was to elucidate possible mechanisms of phthalimide neovascular ...
  • The genome of the polar eukaryotic microalga coccomyxa subellipsoidea reveals traits of cold adaptation 

    Blanc, Guillaume; Agarkova, Irina; Grimwood, Jane; Kuo, Alan; Brueggeman, Andrew; Dunigan, David D.; Gurnon, James; Ladunga, Istvan; Lindquist, Erika; Lucas, Susan; Pangilinan, Jasmyn; Pröschold, Thomas; Salamov, Asaf; Schmutz, Jeremy; Weeks, Donald; Yamada, Takashi; Lomsadze, Alexandre; Borodovsky, Mark; Claverie, Jean-Michel; Grigoriev, Igor V.; Van Etten, James L. (Georgia Institute of TechnologyBioMed Central, 2012)
    Background: Little is known about the mechanisms of adaptation of life to the extreme environmental conditions encountered in polar regions. Here we present the genome sequence of a unicellular green alga from the division ...
  • An asynchronous architecture for modeling intersegmental neural communication 

    Patel, Girish N.; Reid, Michael S.; Schimmel, David E.; DeWeerth, Stephen P. (Georgia Institute of TechnologyInstitute of Electrical and Electronics Engineers, 2006-02)
    This paper presents an asynchronous VLSI architecture for modeling the oscillatory patterns seen in segmented biological systems. The architecture emulates the intersegmental synaptic connectivity observed in these biological ...
  • Wavy-Walled Bioreactor Supports Increased Cell Proliferation and Matrix Deposition in Engineered Cartilage Constructs 

    Bueno, Ericka M.; Bilgen, Bahar; Barabino, Gilda A. (Georgia Institute of TechnologyMary Ann Liebert, Inc., 2005-11)
    Hydrodynamic forces in bioreactors can decisively influence extracellular matrix deposition in engineered cartilage constructs. In the present study, the reduced fluid shear, high-axial mixing environment provided by a ...
  • An analog VLSI model of muscular contraction 

    Hudson, Tina A.; Bragg, Julian A.; Hasler, Paul; DeWeerth, Stephen P. (Georgia Institute of TechnologyInstitute of Electrical and Electronics Engineers, 2003-07)
    We have developed analog VLSI circuits to model the behavior demonstrated by biological sarcomeres, the force generating components of muscle tissue. The circuits are based upon the mathematical description of crossbridge ...
  • Tracking Retinal Motion with a Scanning Laser Ophthalmoscope 

    Xu, Zhiheng; Schuchard, David Ross; Benkeser, Paul J. (Georgia Institute of TechnologyU.S. Department of Veterans Affairs, 2005)
    MathWorks, Natick, MA) software. The new software technique was experimentally tested on both normal- and low-vision subjects and compared with the results obtained using manual techniques. The findings indicate that the ...
  • The Chlorella variabilis NC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex 

    Blanc, Guillaume; Duncan, Garry; Agarkova, Irina; Borodovsky, Mark; Gurnon, James; Kuo, Ala; Lindquist, Erika; Lucas, Susan; Pangilinan, Jasmyn; Polle, Juergen; Salamov, Asaf; Terry, Astrid; Yamada, Takashi; Dunigan, David D.; Grigoriev, Igor V.; Claverie, Jean-Michel; Van Etten, James L. (Georgia Institute of TechnologyAmerican Society of Plant Physiologists, 2010-09)
    Chlorella variabilis NC64A, a unicellular photosynthetic green alga (Trebouxiophyceae), is an intracellular photobiont of Paramecium bursaria and a model system for studying virus/algal interactions. We sequenced its 46-Mb ...
  • Modeling alternation to synchrony with inhibitory coupling: A neuromorphic VLSI approach 

    Cymbalyuk, Gennady S.; Patel, Girish N.; Calabrese, Ronald L.; DeWeerth, Stephen P.; Cohen, Avis H. (Georgia Institute of TechnologyMIT Press, 2000)
    We developed an analog very large-scale integrated system of two mutually inhibitory silicon neurons that display several different stable oscillations. For example, oscillations can be synchronous with weak inhibitory ...
  • Ab initio Gene Identification in Metagenomic Sequences 

    Zhu, Wenhan; Lomsadze, Alexandre; Borodovsky, Mark (Georgia Institute of TechnologyOxford University Press, 2010)
    We describe an algorithm for gene identification in DNA sequences derived from shotgun sequencing of microbial communities. Accurate ab initio gene prediction in a short nucleotide sequence of anonymous origin is hampered ...
  • Dual FRET molecular beacons for mRNA detection in living cells 

    Santangelo, Philip J.; Nix, Brent; Tsourkas, Andrew; Bao, Gang (Georgia Institute of TechnologyOxford University Press, 2004)
    The ability to visualize in real-time the expression level and localization of specific endogenous RNAs in living cells can offer tremendous opportunities for biological and disease studies. Here we demonstrate such a ...
  • Sensory feedback in a half-center oscillator model 

    Simoni, Mario R.; DeWeerth, Stephen P. (Georgia Institute of TechnologyInstitute of Electrical and Electronics Engineers, 2007-02)
    We hypothesize that one role of sensorimotor feedback for rhythmic movements in biological organisms is to synchronize the frequency of movements to the mechanical resonance of the body. Our hypothesis is based on recent ...

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